BayesPeak: Bayesian Analysis of ChIP-seq Data
Version 1.28.0

This package is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data.

AuthorChristiana Spyrou, Jonathan Cairns, Rory Stark, Andy Lynch, Simon Tavar\\'{e},
Bioconductor views ChIPSeq
Date of publicationNone
MaintainerJonathan Cairns <jonathan.cairns@babraham.ac.uk>
LicenseGPL (>= 2)
Version1.28.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BayesPeak")

Popular man pages

overfitting: Overfitting diagnostic functions
plot.job: Plot the called peaks in a job.
plot.PP: Job PP plot.
raw.output: Example raw.output object
raw.output.H3K4me3: Example raw.output object from H3K4me3 data
read.bed: BayesPeak - Bayesian analysis of ChIP-seq data
summarise.peaks: Summarize Peaks
See all...

All man pages Function index File listing

Man pages

bayespeak: BayesPeak - Bayesian analysis of ChIP-seq data
overfitting: Overfitting diagnostic functions
plot.bed: Plot bed file.
plot.job: Plot the called peaks in a job.
plot.PP: Job PP plot.
raw.output: Example raw.output object
raw.output.H3K4me3: Example raw.output object from H3K4me3 data
read.bed: BayesPeak - Bayesian analysis of ChIP-seq data
summarise.peaks: Summarize Peaks

Functions

IsInPolygon Source code
autocov Source code
bayespeak Man page Source code
bin.strand Source code
identify.overfitdiag Man page Source code
plot.PP Man page Source code
plot.bed Man page Source code
plot.job Man page Source code
plot.overfitdiag Man page Source code
raw.output Man page
raw.output.H3K4me3 Man page
read.bed Man page Source code
region.overfitdiag Man page Source code
seqcover Source code
strand.split Source code
summarise.peaks Man page Source code
summarize.peaks Man page
take.union Source code

Files

DESCRIPTION
NAMESPACE
R
R/bayespeak.R
R/overfitting.R
R/visuals.R
build
build/vignette.rds
data
data/datalist
data/raw.output.H3K4me3.rda
data/raw.output.rda
inst
inst/CITATION
inst/doc
inst/doc/BayesPeak.R
inst/doc/BayesPeak.Rnw
inst/doc/BayesPeak.pdf
inst/extdata
inst/extdata/H3K4me3reduced.bed
inst/extdata/Inputreduced.bed
man
man/bayespeak.Rd
man/overfitting.Rd
man/plot.PP.Rd
man/plot.bed.Rd
man/plot.job.Rd
man/raw.output.H3K4me3.Rd
man/raw.output.Rd
man/read.bed.Rd
man/summarise.peaks.Rd
src
src/bayespeak.c
src/bayespeak_gsl.h
vignettes
vignettes/BayesPeak.Rnw
vignettes/BayesPeak.bib
vignettes/OF.png
vignettes/changelog.txt
vignettes/regionOFdiag.pdf
BayesPeak documentation built on May 20, 2017, 9:44 p.m.

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